FMO DATABASE

FMODB ID: Q1KJY

Calculation Name: 1BM9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1BM9

Chain ID: A

ChEMBL ID:

UniProt ID: P0CI76

Base Structure: X-ray

Registration Date: 2023-03-13

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	120
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1018711.99383
FMO2-HF: Nuclear repulsion	969420.857178
FMO2-HF: Total energy	-49291.136652
FMO2-MP2: Total energy	-49436.723793

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:3:GLU)

Summations of interaction energy for fragment #1(A:3:GLU)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-300.947	-306.376	33.767	-15.088	-13.25	0.169

Interaction energy analysis for fragmet #1(A:3:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.770 / q_NPA : -0.852

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

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Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	5	LYS	1	0.933	0.959	3.254	-45.299	-41.449	0.408	-2.027	-2.231	0.008
4	A	6	ARG	1	0.888	0.933	1.713	-152.287	-162.100	33.335	-12.932	-10.590	0.157
5	A	7	SER	0	-0.003	-0.003	3.626	-8.223	-7.772	0.025	-0.122	-0.354	0.004
6	A	8	SER	0	-0.007	-0.002	4.706	-2.931	-2.848	-0.001	-0.007	-0.075	0.000
7	A	9	THR	0	-0.038	-0.023	7.178	1.136	1.136	0.000	0.000	0.000	0.000
8	A	10	GLY	0	0.050	0.037	9.843	-1.577	-1.577	0.000	0.000	0.000	0.000
9	A	11	PHE	0	0.023	0.005	13.552	0.263	0.263	0.000	0.000	0.000	0.000
10	A	12	LEU	0	0.023	0.010	14.473	1.230	1.230	0.000	0.000	0.000	0.000
11	A	13	VAL	0	0.055	0.023	15.167	0.775	0.775	0.000	0.000	0.000	0.000
12	A	14	LYS	1	0.949	0.969	17.736	-15.952	-15.952	0.000	0.000	0.000	0.000
13	A	15	GLN	0	0.078	0.030	21.216	-0.146	-0.146	0.000	0.000	0.000	0.000
14	A	16	ARG	1	0.877	0.911	23.495	-12.329	-12.329	0.000	0.000	0.000	0.000
15	A	17	ALA	0	0.006	0.015	18.548	-0.090	-0.090	0.000	0.000	0.000	0.000
16	A	18	PHE	0	0.018	0.008	19.013	0.345	0.345	0.000	0.000	0.000	0.000
17	A	19	LEU	0	-0.017	-0.021	20.760	-0.201	-0.201	0.000	0.000	0.000	0.000
18	A	20	LYS	1	0.868	0.934	21.643	-14.319	-14.319	0.000	0.000	0.000	0.000
19	A	21	LEU	0	0.027	0.026	16.884	-0.170	-0.170	0.000	0.000	0.000	0.000
20	A	22	TYR	0	0.048	0.017	20.679	-0.089	-0.089	0.000	0.000	0.000	0.000
21	A	23	MET	0	-0.027	-0.004	23.389	-0.403	-0.403	0.000	0.000	0.000	0.000
22	A	24	ILE	0	0.004	0.014	20.983	-0.409	-0.409	0.000	0.000	0.000	0.000
23	A	25	THR	0	-0.002	-0.008	21.577	-0.086	-0.086	0.000	0.000	0.000	0.000
24	A	26	MET	0	-0.047	-0.026	23.712	-0.473	-0.473	0.000	0.000	0.000	0.000
25	A	27	THR	0	-0.051	-0.030	26.801	-0.571	-0.571	0.000	0.000	0.000	0.000
26	A	28	GLU	-1	-0.806	-0.868	22.125	13.985	13.985	0.000	0.000	0.000	0.000
27	A	29	GLN	0	-0.025	0.005	25.977	-0.351	-0.351	0.000	0.000	0.000	0.000
28	A	30	GLU	-1	-0.934	-0.949	29.108	8.994	8.994	0.000	0.000	0.000	0.000
29	A	31	ARG	1	0.809	0.880	27.700	-10.910	-10.910	0.000	0.000	0.000	0.000
30	A	32	LEU	0	-0.023	-0.004	28.857	-0.069	-0.069	0.000	0.000	0.000	0.000
31	A	33	TYR	0	0.002	-0.011	32.206	-0.192	-0.192	0.000	0.000	0.000	0.000
32	A	34	GLY	0	-0.017	-0.017	35.666	0.066	0.066	0.000	0.000	0.000	0.000
33	A	35	LEU	0	-0.005	0.003	36.345	0.182	0.182	0.000	0.000	0.000	0.000
34	A	36	LYS	1	0.992	0.999	36.452	-8.703	-8.703	0.000	0.000	0.000	0.000
35	A	37	LEU	0	0.013	0.018	30.339	0.118	0.118	0.000	0.000	0.000	0.000
36	A	38	LEU	0	-0.011	-0.009	32.944	0.273	0.273	0.000	0.000	0.000	0.000
37	A	39	GLU	-1	-0.867	-0.951	33.902	8.667	8.667	0.000	0.000	0.000	0.000
38	A	40	VAL	0	-0.004	-0.007	31.587	-0.020	-0.020	0.000	0.000	0.000	0.000
39	A	41	LEU	0	0.000	-0.001	27.593	0.247	0.247	0.000	0.000	0.000	0.000
40	A	42	ARG	1	0.835	0.902	29.817	-8.947	-8.947	0.000	0.000	0.000	0.000
41	A	43	SER	0	-0.003	0.005	32.021	0.038	0.038	0.000	0.000	0.000	0.000
42	A	44	GLU	-1	-0.844	-0.894	26.959	10.557	10.557	0.000	0.000	0.000	0.000
43	A	45	PHE	0	-0.021	-0.014	23.997	0.302	0.302	0.000	0.000	0.000	0.000
44	A	46	LYS	1	0.828	0.888	28.661	-9.373	-9.373	0.000	0.000	0.000	0.000
45	A	47	GLU	-1	-0.833	-0.895	28.687	9.699	9.699	0.000	0.000	0.000	0.000
46	A	48	ILE	0	-0.031	-0.017	24.658	0.002	0.002	0.000	0.000	0.000	0.000
47	A	49	GLY	0	0.058	0.044	28.088	0.058	0.058	0.000	0.000	0.000	0.000
48	A	50	PHE	0	-0.068	-0.022	25.693	0.047	0.047	0.000	0.000	0.000	0.000
49	A	51	LYS	1	0.934	0.953	28.698	-9.850	-9.850	0.000	0.000	0.000	0.000
50	A	52	PRO	0	-0.009	0.013	28.237	-0.042	-0.042	0.000	0.000	0.000	0.000
51	A	53	ASN	0	0.052	0.009	29.925	-0.613	-0.613	0.000	0.000	0.000	0.000
52	A	54	HIS	0	0.038	0.010	31.829	0.320	0.320	0.000	0.000	0.000	0.000
53	A	55	THR	0	0.056	0.021	33.569	0.134	0.134	0.000	0.000	0.000	0.000
54	A	56	GLU	-1	-0.798	-0.893	26.893	12.236	12.236	0.000	0.000	0.000	0.000
55	A	57	VAL	0	0.008	0.023	28.973	0.348	0.348	0.000	0.000	0.000	0.000
56	A	58	TYR	0	0.025	0.016	30.490	0.156	0.156	0.000	0.000	0.000	0.000
57	A	59	ARG	1	0.880	0.929	28.891	-10.831	-10.831	0.000	0.000	0.000	0.000
58	A	60	SER	0	-0.005	-0.026	25.896	0.386	0.386	0.000	0.000	0.000	0.000
59	A	61	LEU	0	0.014	0.003	26.945	0.277	0.277	0.000	0.000	0.000	0.000
60	A	62	HIS	0	-0.021	-0.010	29.404	-0.252	-0.252	0.000	0.000	0.000	0.000
61	A	63	GLU	-1	-0.709	-0.825	25.210	12.903	12.903	0.000	0.000	0.000	0.000
62	A	64	LEU	0	0.008	0.012	22.913	0.279	0.279	0.000	0.000	0.000	0.000
63	A	65	LEU	0	-0.065	-0.031	26.280	-0.021	-0.021	0.000	0.000	0.000	0.000
64	A	66	ASP	-1	-0.926	-0.973	29.096	10.288	10.288	0.000	0.000	0.000	0.000
65	A	67	ASP	-1	-0.943	-0.968	23.547	13.648	13.648	0.000	0.000	0.000	0.000
66	A	68	GLY	0	-0.084	-0.046	25.222	0.208	0.208	0.000	0.000	0.000	0.000
67	A	69	ILE	0	0.024	0.018	21.353	0.003	0.003	0.000	0.000	0.000	0.000
68	A	70	LEU	0	-0.004	0.001	25.427	-0.187	-0.187	0.000	0.000	0.000	0.000
69	A	71	LYS	1	0.940	0.968	28.557	-9.889	-9.889	0.000	0.000	0.000	0.000
70	A	72	GLN	0	0.004	-0.013	32.216	-0.136	-0.136	0.000	0.000	0.000	0.000
71	A	73	ILE	0	-0.003	0.007	35.327	-0.151	-0.151	0.000	0.000	0.000	0.000
72	A	74	LYS	1	0.847	0.914	38.055	-7.763	-7.763	0.000	0.000	0.000	0.000
73	A	75	VAL	0	0.039	0.021	41.214	-0.092	-0.092	0.000	0.000	0.000	0.000
74	A	76	LYS	1	0.872	0.924	44.513	-6.942	-6.942	0.000	0.000	0.000	0.000
75	A	77	LYS	1	0.944	0.962	46.856	-6.753	-6.753	0.000	0.000	0.000	0.000
76	A	78	GLU	-1	-0.873	-0.937	49.040	6.106	6.106	0.000	0.000	0.000	0.000
77	A	79	GLY	0	-0.028	0.001	52.541	-0.119	-0.119	0.000	0.000	0.000	0.000
78	A	80	ALA	0	-0.046	-0.035	50.806	-0.024	-0.024	0.000	0.000	0.000	0.000
79	A	81	LYS	1	1.023	1.022	51.566	-5.627	-5.627	0.000	0.000	0.000	0.000
80	A	82	LEU	0	-0.033	-0.031	49.931	0.029	0.029	0.000	0.000	0.000	0.000
81	A	83	GLN	0	0.035	0.037	45.401	0.262	0.262	0.000	0.000	0.000	0.000
82	A	84	GLU	-1	-0.796	-0.893	42.978	7.277	7.277	0.000	0.000	0.000	0.000
83	A	85	VAL	0	0.008	0.011	41.095	0.112	0.112	0.000	0.000	0.000	0.000
84	A	86	VAL	0	-0.012	-0.006	36.680	0.027	0.027	0.000	0.000	0.000	0.000
85	A	87	LEU	0	0.027	0.021	34.528	0.073	0.073	0.000	0.000	0.000	0.000
86	A	88	TYR	0	-0.011	-0.004	31.089	-0.056	-0.056	0.000	0.000	0.000	0.000
87	A	89	GLN	0	0.044	0.014	30.751	0.015	0.015	0.000	0.000	0.000	0.000
88	A	90	PHE	0	0.038	0.004	24.385	0.088	0.088	0.000	0.000	0.000	0.000
89	A	91	LYS	1	0.818	0.929	27.968	-11.095	-11.095	0.000	0.000	0.000	0.000
90	A	92	ASP	-1	-0.785	-0.897	23.172	13.689	13.689	0.000	0.000	0.000	0.000
91	A	93	TYR	0	-0.028	-0.046	22.363	0.513	0.513	0.000	0.000	0.000	0.000
92	A	94	GLU	-1	-0.759	-0.859	20.048	15.589	15.589	0.000	0.000	0.000	0.000
93	A	95	ALA	0	0.016	0.013	18.697	1.192	1.192	0.000	0.000	0.000	0.000
94	A	96	ALA	0	-0.021	-0.017	18.639	0.872	0.872	0.000	0.000	0.000	0.000
95	A	97	LYS	1	0.804	0.877	17.612	-14.445	-14.445	0.000	0.000	0.000	0.000
96	A	98	LEU	0	-0.038	-0.018	13.183	1.595	1.595	0.000	0.000	0.000	0.000
97	A	99	TYR	0	0.006	0.013	13.960	1.730	1.730	0.000	0.000	0.000	0.000
98	A	100	LYS	1	0.877	0.912	15.064	-14.487	-14.487	0.000	0.000	0.000	0.000
99	A	101	LYS	1	0.934	0.983	10.395	-23.033	-23.033	0.000	0.000	0.000	0.000
100	A	102	GLN	0	0.003	-0.017	10.283	1.143	1.143	0.000	0.000	0.000	0.000
101	A	103	LEU	0	0.004	-0.001	11.179	1.352	1.352	0.000	0.000	0.000	0.000
102	A	104	LYS	1	0.871	0.936	8.287	-25.958	-25.958	0.000	0.000	0.000	0.000
103	A	105	VAL	0	0.026	0.012	6.095	-0.036	-0.036	0.000	0.000	0.000	0.000
104	A	106	GLU	-1	-0.822	-0.870	8.403	27.954	27.954	0.000	0.000	0.000	0.000
105	A	107	LEU	0	0.025	0.017	11.224	-0.937	-0.937	0.000	0.000	0.000	0.000
106	A	108	ASP	-1	-0.792	-0.888	7.380	26.139	26.139	0.000	0.000	0.000	0.000
107	A	109	ARG	1	0.713	0.844	8.433	-27.442	-27.442	0.000	0.000	0.000	0.000
108	A	110	CYS	0	-0.051	-0.020	9.389	-1.772	-1.772	0.000	0.000	0.000	0.000
109	A	111	LYS	1	0.825	0.893	11.499	-19.354	-19.354	0.000	0.000	0.000	0.000
110	A	112	LYS	1	0.929	0.945	6.127	-32.108	-32.108	0.000	0.000	0.000	0.000
111	A	113	LEU	0	-0.017	0.005	11.554	-0.857	-0.857	0.000	0.000	0.000	0.000
112	A	114	ILE	0	-0.003	-0.008	14.026	-1.019	-1.019	0.000	0.000	0.000	0.000
113	A	115	GLU	-1	-0.785	-0.878	13.728	17.114	17.114	0.000	0.000	0.000	0.000
114	A	116	LYS	1	0.805	0.896	14.365	-17.887	-17.887	0.000	0.000	0.000	0.000
115	A	117	ALA	0	0.000	-0.001	16.290	-0.802	-0.802	0.000	0.000	0.000	0.000
116	A	118	LEU	0	0.006	0.001	19.258	-0.754	-0.754	0.000	0.000	0.000	0.000
117	A	119	SER	0	0.007	0.002	18.850	-0.571	-0.571	0.000	0.000	0.000	0.000
118	A	120	ASP	-1	-0.869	-0.917	19.294	15.510	15.510	0.000	0.000	0.000	0.000
119	A	121	ASN	0	-0.095	-0.055	21.780	-0.722	-0.722	0.000	0.000	0.000	0.000
120	A	122	PHE	0	-0.030	0.015	24.275	-0.751	-0.751	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:GLU)